Back to selection
79701-01 - Seminar: Introduction to Plant Image Analysis (1 CP)
| Semester | fall semester 2026 |
| Course frequency | Every fall sem. |
| Lecturers |
Atena Haghighattalab (atena.haghighattalab@unibas.ch)
Guillaume Lobet (guillaume.lobet@unibas.ch) Niklas Peter Schandry (niklaspeter.schandry@unibas.ch) |
| Content | This seminar is tailored for PhD students in plant sciences with little or no experience in plant image analysis, who want to learn how to analyse their plant images. The seminar will focus on acquiring and analysing images of individual plants (shoots, roots). Note that imaging on larger scales (e.g. crop fields via remote sensing) or smaller scales (e.g. fluorescent microscopy of tissues or cells) will not be the focus of this course. Over three days, three experts in plant imaging will introduce different aspects of imaging (image acquisition, image processing, image analysis, data extraction, …) and will provide demonstrations or hands-on exercises. At the end of each day, students will have the opportunity to come with their own questions and problems on plant imaging to receive tailored advice from the experts. |
| Learning objectives | - Students will know about different sensors for image acquisition - Students can design an imaging experiment aligned with a defined biological hypothesis - Students can recognize key factors affecting RGB image quality - Students can extract and interpret basic quantitative traits from plant images - Students can critically evaluate when additional imaging modalities may be scientifically justified - Students will know what to consider when acquiring images for analysis, and how images can be processed - Students will know about tools and software that can be used for image analysis - Students will understand the relationship between measurements and biological traits |
| Admission requirements | No prior knowledge on image analysis is required. Basic knowledge of R (for example, attendance of the PSC course “Introduction to R”) is beneficial, but not required. Priority is given to PSC PhD students. Please register for the course at least two weeks before the start date. |
| Language of instruction | English |
| Use of digital media | No specific media used |
| Interval | Weekday | Time | Room |
|---|---|---|---|
| Block | See individual dates | ||
Dates
| Date | Time | Room |
|---|---|---|
| Thursday 01.10.2026 | 09.00-17.00 | Alte Universität, Besprechung 003 |
| Friday 02.10.2026 | 09.00-17.00 | Kollegienhaus, Mehrzweckraum 035 |
| Monday 05.10.2026 | 09.00-17.00 | Kollegienhaus, Mehrzweckraum 035 |
| Modules |
Courses: Master's Studies Plant Science (Master's Studies: Plant Science (Start of studies before 01.08.2025)) Doctorate Botany: Recommendations (PhD subject: Botany) Module: Courses for Master's Studies in Plant Science (Master's Studies: Plant Science) |
| Assessment format | continuous assessment |
| Assessment details | Active participation and attendance during all three days are required. |
| Assessment registration/deregistration | Reg.: course registration, dereg: cancel course registration |
| Repeat examination | no repeat examination |
| Scale | Pass / Fail |
| Repeated registration | as often as necessary |
| Responsible faculty | Faculty of Science, studiendekanat-philnat@unibas.ch |
| Offered by | Integrative Biologie |